It really is complicated from how I see it. The intention and reasoning for these darker skinned villains aren't atleast usually because POC would be considered evil (I would hope). There are other factors like the mentioned night vs day, religious texts. And it's not just dark skin that is used for villains, it also traditionally shows in black clothing. Like Sephiroth, Palpatine, Maleficent, heck even Cobra Kai in Karate Kid. Color black is associated with darkness, decay, corruption and death. In many cultures it's a custom to wear black at funerals.
Now can these darker skinned villains be associated with people of color, well easily as we can see in this thread. And it comes even more problematic when kids who don't have or understand the full context and reasoning behind it. It can enforce harmful stereotypes and shape the world view of people even subconsciously. I don't have a solution to fixing it, other than stop doing it. But is that the right solution either if the problem stems from misconception. In the current climate, it could be almost necessary. It wouldn't remove the problems and difficulties people face because of their skin color. But in long term it could help to alleviate it.
